3M96

Crystal structure of human carbonic anhydrase isozyme II with 5-{[(5-bromo-1H-benzimidazol-2-yl)sulfanyl]acetyl}-2-chlorobenzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb3M96/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-20 Released: 2011-02-02 
• Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.213 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 

Starting Model: experimental

Literature

Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII.

Baranauskiene, L., Golovenko, D., Manakova, E., Grazulis, S., Tumkevicius, S., Matulis, D.

(2010) Bioorg Med Chem 18: 7357-7364

• PubMed: 20926301 
• DOI: https://doi.org/10.1016/j.bmc.2010.09.016
• Primary Citation of Related Structures:  
  3M67, 3M96, 3MYQ


• PubMed Abstract: 
  

  A series of novel 2-chloro-5-[(1-benzimidazolyl- and 2-benzimidazolylsulfanyl)acetyl]benzene-sulfonamides were designed and synthesized. Their binding to recombinant human carbonic anhydrase (hCA) isozymes I, II, VII, and XIII was determined by isothermal titration calorimetry and thermal shift assay. The designed S-alkylated benzimidazole derivatives exhibited stronger binding than the indapamide-like N-alkylated benzimidazoles, with the K(d) reaching about 50-100 nM with drug-targeted hCAs VII and XIII. The cocrystal structures of selected compounds with hCA II were determined by X-ray crystallography, and structural features of the binding event were revealed.

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Organizational Affiliation: 

Laboratory of Biothermodynamics and Drug Design, Institute of Biotechnology, Graičiūno 8, Vilnius LT-02241, Lithuania.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.97 kDa 
• Atom Count: 2,362 
• Modelled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E38	E [auth A]	5-{[(5-bromo-1H-benzimidazol-2-yl)sulfanyl]acetyl}-2-chlorobenzenesulfonamide C15 H11 Br Cl N3 O3 S2 ABLVCEKUEJSYQL-UHFFFAOYSA-N
DMS	C [auth A], D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E38	PDBBind:  3M96	Kd: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.213 
• R-Value Work: 0.176 
• R-Value Observed: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.05	α = 90
b = 40.921	β = 104.14
c = 71.468	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-02 
Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

Revision History  

• Version 1.0: 2011-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description